[Chimera-users] Four letter residue names

[Elaine Meng]

Hi Francesco,
Short answer since I'm theoretically not at work today, but yes Chimera reads and allows 4-character residue names, even though the PDB standard format description is only for 3-character names.  

This is mentioned in the "intro to PDB format" in the Chimera User Guide:

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note5>  

Not much else to say about it though.  I don't know what you mean by the "scope" or how to modify the file for CHARMM or other programs.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Apr 21, 2021, at 7:17 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
> 
> Hi all
> A pdb file deriving from a mmCIF file (with chimerax) and comprising both nucleotides and proteins, shows the protein residue names with four characters (i.e., using also column 21), such as ALAM in one subunit, or GLNm in another subunit.
> 
> I read on passing somewhere (and I am unable to trace that back) that chimera accepts such four character names but was unable to find a description from chimera help. I also got lost in deciphering the intricacies of mmCIF files.  What is the scope of the column 21 character? Could that simply be ignored, or deleted, for use with the CHARMM FF?
> 
> Thanks for advice
> 
> francesco pietra